data_3Y0 # _chem_comp.id 3Y0 _chem_comp.name "[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3R,4R,5R)-3-oxidanyl-5-sulfanyl-4-tridecoxy-oxolan-2-yl]methyl hydrogen phosphate" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C28 H49 N5 O13 P2 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2014-12-09 _chem_comp.pdbx_modified_date 2016-01-08 _chem_comp.pdbx_ambiguous_flag N _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ? _chem_comp.formula_weight 757.727 _chem_comp.one_letter_code ? _chem_comp.three_letter_code ? _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 4X3O _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.alt_atom_id _chem_comp_atom.type_symbol _chem_comp_atom.charge _chem_comp_atom.pdbx_align _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_leaving_atom_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.model_Cartn_x _chem_comp_atom.model_Cartn_y _chem_comp_atom.model_Cartn_z _chem_comp_atom.pdbx_model_Cartn_x_ideal _chem_comp_atom.pdbx_model_Cartn_y_ideal _chem_comp_atom.pdbx_model_Cartn_z_ideal _chem_comp_atom.pdbx_component_atom_id _chem_comp_atom.pdbx_component_comp_id _chem_comp_atom.pdbx_ordinal 3Y0 O2N O1 O 0 1 N N N 0.303 1.278 19.000 -2.579 -4.819 -1.865 O2N 3Y0 1 3Y0 PN P1 P 0 1 N N N 0.198 2.513 18.169 -2.154 -3.969 -0.565 PN 3Y0 2 3Y0 O1N O2 O 0 1 N N N 1.141 3.642 18.472 -1.988 -4.882 0.589 O1N 3Y0 3 3Y0 O3 O3 O 0 1 N N N -1.301 3.121 18.242 -3.300 -2.888 -0.233 O3 3Y0 4 3Y0 PA P2 P 0 1 N N N -2.707 2.337 18.438 -4.727 -2.963 0.509 PA 3Y0 5 3Y0 O5B O4 O 0 1 N N N -2.759 2.072 20.027 -5.223 -1.474 0.868 O5B 3Y0 6 3Y0 C5B C1 C 0 1 N N N -2.942 3.162 20.911 -6.407 -1.209 1.623 C5B 3Y0 7 3Y0 C4B C2 C 0 1 N N R -3.053 2.629 22.332 -6.585 0.302 1.780 C4B 3Y0 8 3Y0 O4B O5 O 0 1 N N N -3.137 3.743 23.229 -6.925 0.904 0.512 O4B 3Y0 9 3Y0 C1B C3 C 0 1 N N R -4.310 3.593 24.091 -7.539 2.168 0.843 C1B 3Y0 10 3Y0 N9A N1 N 0 1 Y N N -4.631 4.973 24.422 -8.354 2.648 -0.276 N9A 3Y0 11 3Y0 C8A C4 C 0 1 Y N N -5.053 5.967 23.580 -8.908 1.880 -1.257 C8A 3Y0 12 3Y0 N7A N2 N 0 1 Y N N -5.092 7.130 24.268 -9.568 2.632 -2.090 N7A 3Y0 13 3Y0 C5A C5 C 0 1 Y N N -4.608 6.884 25.511 -9.481 3.925 -1.696 C5A 3Y0 14 3Y0 C6A C6 C 0 1 Y N N -4.386 7.689 26.612 -9.977 5.144 -2.190 C6A 3Y0 15 3Y0 N6A N3 N 0 1 N N N -4.644 9.033 26.617 -10.752 5.181 -3.336 N6A 3Y0 16 3Y0 N1A N4 N 0 1 Y N N -3.884 7.120 27.716 -9.686 6.260 -1.530 N1A 3Y0 17 3Y0 C2A C7 C 0 1 Y N N -3.622 5.795 27.757 -8.948 6.234 -0.435 C2A 3Y0 18 3Y0 N3A N5 N 0 1 Y N N -3.830 4.979 26.720 -8.462 5.117 0.064 N3A 3Y0 19 3Y0 C4A C8 C 0 1 Y N N -4.323 5.524 25.583 -8.706 3.950 -0.525 C4A 3Y0 20 3Y0 C2B C9 C 0 1 N N R -5.274 2.817 23.241 -8.431 1.866 2.068 C2B 3Y0 21 3Y0 O2B O6 O 0 1 N N N -6.229 2.234 24.109 -8.404 2.958 2.988 O2B 3Y0 22 3Y0 C3B C10 C 0 1 N N S -4.355 1.838 22.513 -7.788 0.610 2.698 C3B 3Y0 23 3Y0 O3B O7 O 0 1 N N N -4.070 0.675 23.297 -7.346 0.888 4.028 O3B 3Y0 24 3Y0 O1A O8 O 0 1 N N N -2.636 0.969 17.827 -4.595 -3.752 1.754 O1A 3Y0 25 3Y0 O2A O9 O 0 1 N N N -3.757 3.346 18.027 -5.800 -3.667 -0.462 O2A 3Y0 26 3Y0 O5D O10 O 0 1 N N N 0.197 2.131 16.608 -0.764 -3.208 -0.851 O5D 3Y0 27 3Y0 C5D C11 C 0 1 N N N 1.359 1.562 16.007 0.468 -3.896 -1.074 C5D 3Y0 28 3Y0 C4D C12 C 0 1 N N R 1.522 2.065 14.586 1.584 -2.878 -1.314 C4D 3Y0 29 3Y0 C3D C13 C 0 1 N N R 1.812 3.545 14.449 2.893 -3.609 -1.671 C3D 3Y0 30 3Y0 O3D O11 O 0 1 N N N 3.118 3.934 14.805 3.398 -3.146 -2.926 O3D 3Y0 31 3Y0 C2D C14 C 0 1 N N R 1.542 3.738 12.965 3.863 -3.233 -0.525 C2D 3Y0 32 3Y0 C1D C15 C 0 1 N N R 0.276 2.929 12.856 2.886 -2.806 0.600 C1D 3Y0 33 3Y0 O4D O12 O 0 1 N N N 0.359 1.846 13.765 1.826 -2.126 -0.113 O4D 3Y0 34 3Y0 S1 S1 S 0 1 N N N 0.097 2.240 11.234 3.703 -1.674 1.759 S1 3Y0 35 3Y0 O2D O13 O 0 1 N N N 2.620 3.137 12.231 4.708 -2.146 -0.908 O2D 3Y0 36 3Y0 C1 C16 C 0 1 N N N 3.027 3.661 10.950 5.994 -2.162 -0.284 C1 3Y0 37 3Y0 C2 C17 C 0 1 N N N 3.218 5.180 10.893 6.808 -0.959 -0.765 C2 3Y0 38 3Y0 C3 C18 C 0 1 N N N 2.121 5.815 10.056 8.185 -0.976 -0.097 C3 3Y0 39 3Y0 C4 C19 C 0 1 N N N 2.168 7.335 10.243 9.000 0.226 -0.578 C4 3Y0 40 3Y0 C5 C20 C 0 1 N N N 0.932 8.012 9.696 10.377 0.209 0.090 C5 3Y0 41 3Y0 C6 C21 C 0 1 N N N 1.052 9.523 9.800 11.191 1.412 -0.391 C6 3Y0 42 3Y0 C7 C22 C 0 1 N N N -0.266 10.189 9.406 12.568 1.395 0.276 C7 3Y0 43 3Y0 C8 C23 C 0 1 N N N -0.092 11.680 9.131 13.383 2.597 -0.204 C8 3Y0 44 3Y0 C9 C24 C 0 1 N N N 0.270 12.450 10.398 14.759 2.580 0.463 C9 3Y0 45 3Y0 C10 C25 C 0 1 N N N 0.290 13.973 10.230 15.574 3.783 -0.017 C10 3Y0 46 3Y0 C11 C26 C 0 1 N N N 0.802 14.637 11.521 16.951 3.766 0.650 C11 3Y0 47 3Y0 C12 C27 C 0 1 N N N 1.806 15.761 11.282 17.765 4.968 0.170 C12 3Y0 48 3Y0 C13 C28 C 0 1 N N N 2.802 15.960 12.415 19.142 4.951 0.837 C13 3Y0 49 3Y0 H1 H1 H 0 1 N N N 0.994 1.386 19.643 -2.705 -4.284 -2.660 H1 3Y0 50 3Y0 H2 H2 H 0 1 N N N -2.083 3.845 20.839 -7.271 -1.624 1.102 H2 3Y0 51 3Y0 H3 H3 H 0 1 N N N -3.863 3.702 20.646 -6.321 -1.669 2.607 H3 3Y0 52 3Y0 H4 H4 H 0 1 N N N -2.189 1.989 22.565 -5.676 0.750 2.183 H4 3Y0 53 3Y0 H5 H5 H 0 1 N N N -4.057 3.022 24.996 -6.777 2.905 1.099 H5 3Y0 54 3Y0 H6 H6 H 0 1 N N N -5.312 5.842 22.539 -8.812 0.807 -1.333 H6 3Y0 55 3Y0 H7 H7 H 0 1 N N N -4.402 9.416 27.508 -10.958 4.359 -3.809 H7 3Y0 56 3Y0 H8 H8 H 0 1 N N N -4.103 9.479 25.904 -11.088 6.028 -3.667 H8 3Y0 57 3Y0 H9 H9 H 0 1 N N N -3.226 5.376 28.670 -8.735 7.164 0.071 H9 3Y0 58 3Y0 H10 H10 H 0 1 N N N -5.754 3.485 22.511 -9.453 1.657 1.753 H10 3Y0 59 3Y0 H11 H11 H 0 1 N N N -6.750 2.918 24.513 -8.947 2.821 3.777 H11 3Y0 60 3Y0 H12 H12 H 0 1 N N N -4.779 1.574 21.533 -8.493 -0.222 2.696 H12 3Y0 61 3Y0 H13 H13 H 0 1 N N N -4.867 0.172 23.419 -8.061 1.089 4.647 H13 3Y0 62 3Y0 H14 H14 H 0 1 N N N -4.316 2.968 17.358 -5.937 -3.203 -1.299 H14 3Y0 63 3Y0 H15 H15 H 0 1 N N N 1.260 0.467 15.994 0.710 -4.501 -0.200 H15 3Y0 64 3Y0 H16 H16 H 0 1 N N N 2.245 1.844 16.595 0.371 -4.541 -1.947 H16 3Y0 65 3Y0 H17 H17 H 0 1 N N N 2.368 1.521 14.140 1.303 -2.203 -2.123 H17 3Y0 66 3Y0 H18 H18 H 0 1 N N N 1.068 4.113 15.026 2.732 -4.686 -1.700 H18 3Y0 67 3Y0 H19 H19 H 0 1 N N N 3.246 3.798 15.736 2.802 -3.303 -3.671 H19 3Y0 68 3Y0 H20 H20 H 0 1 N N N 1.381 4.796 12.712 4.456 -4.095 -0.219 H20 3Y0 69 3Y0 H21 H21 H 0 1 N N N -0.605 3.560 13.045 2.498 -3.679 1.124 H21 3Y0 70 3Y0 H22 H22 H 0 1 N N N -1.026 1.594 11.337 2.735 -1.407 2.654 H22 3Y0 71 3Y0 H23 H23 H 0 1 N N N 2.259 3.387 10.212 5.874 -2.110 0.798 H23 3Y0 72 3Y0 H24 H24 H 0 1 N N N 3.982 3.188 10.678 6.514 -3.082 -0.549 H24 3Y0 73 3Y0 H25 H25 H 0 1 N N N 4.196 5.407 10.443 6.929 -1.011 -1.847 H25 3Y0 74 3Y0 H26 H26 H 0 1 N N N 3.180 5.590 11.913 6.288 -0.039 -0.501 H26 3Y0 75 3Y0 H27 H27 H 0 1 N N N 1.142 5.434 10.381 8.065 -0.925 0.985 H27 3Y0 76 3Y0 H28 H28 H 0 1 N N N 2.277 5.569 8.995 8.706 -1.897 -0.362 H28 3Y0 77 3Y0 H29 H29 H 0 1 N N N 3.051 7.730 9.719 9.120 0.175 -1.660 H29 3Y0 78 3Y0 H30 H30 H 0 1 N N N 2.249 7.558 11.317 8.479 1.147 -0.314 H30 3Y0 79 3Y0 H31 H31 H 0 1 N N N 0.055 7.680 10.271 10.256 0.261 1.172 H31 3Y0 80 3Y0 H32 H32 H 0 1 N N N 0.806 7.732 8.640 10.897 -0.711 -0.175 H32 3Y0 81 3Y0 H33 H33 H 0 1 N N N 1.850 9.871 9.127 11.311 1.360 -1.473 H33 3Y0 82 3Y0 H34 H34 H 0 1 N N N 1.301 9.797 10.836 10.671 2.332 -0.127 H34 3Y0 83 3Y0 H35 H35 H 0 1 N N N -0.988 10.061 10.226 12.448 1.446 1.359 H35 3Y0 84 3Y0 H36 H36 H 0 1 N N N -0.652 9.703 8.498 13.088 0.474 0.012 H36 3Y0 85 3Y0 H37 H37 H 0 1 N N N 0.710 11.815 8.391 13.503 2.546 -1.286 H37 3Y0 86 3Y0 H38 H38 H 0 1 N N N -1.034 12.080 8.728 12.862 3.518 0.060 H38 3Y0 87 3Y0 H39 H39 H 0 1 N N N -0.467 12.199 11.175 14.639 2.632 1.546 H39 3Y0 88 3Y0 H40 H40 H 0 1 N N N 1.270 12.127 10.723 15.280 1.660 0.199 H40 3Y0 89 3Y0 H41 H41 H 0 1 N N N 0.955 14.239 9.395 15.694 3.731 -1.099 H41 3Y0 90 3Y0 H42 H42 H 0 1 N N N -0.728 14.330 10.016 15.053 4.703 0.247 H42 3Y0 91 3Y0 H43 H43 H 0 1 N N N -0.061 15.053 12.062 16.830 3.817 1.732 H43 3Y0 92 3Y0 H44 H44 H 0 1 N N N 1.286 13.866 12.139 17.471 2.845 0.386 H44 3Y0 93 3Y0 H45 H45 H 0 1 N N N 2.368 15.532 10.365 17.885 4.917 -0.912 H45 3Y0 94 3Y0 H46 H46 H 0 1 N N N 1.248 16.699 11.145 17.245 5.889 0.434 H46 3Y0 95 3Y0 H47 H47 H 0 1 N N N 3.485 16.785 12.163 19.722 5.808 0.495 H47 3Y0 96 3Y0 H48 H48 H 0 1 N N N 2.260 16.203 13.341 19.022 5.003 1.919 H48 3Y0 97 3Y0 H49 H49 H 0 1 N N N 3.381 15.036 12.561 19.662 4.031 0.573 H49 3Y0 98 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal 3Y0 C8 C7 SING N N 1 3Y0 C8 C9 SING N N 2 3Y0 C7 C6 SING N N 3 3Y0 C5 C6 SING N N 4 3Y0 C5 C4 SING N N 5 3Y0 C3 C4 SING N N 6 3Y0 C3 C2 SING N N 7 3Y0 C10 C9 SING N N 8 3Y0 C10 C11 SING N N 9 3Y0 C2 C1 SING N N 10 3Y0 C1 O2D SING N N 11 3Y0 S1 C1D SING N N 12 3Y0 C12 C11 SING N N 13 3Y0 C12 C13 SING N N 14 3Y0 O2D C2D SING N N 15 3Y0 C1D C2D SING N N 16 3Y0 C1D O4D SING N N 17 3Y0 C2D C3D SING N N 18 3Y0 O4D C4D SING N N 19 3Y0 C3D C4D SING N N 20 3Y0 C3D O3D SING N N 21 3Y0 C4D C5D SING N N 22 3Y0 C5D O5D SING N N 23 3Y0 O5D PN SING N N 24 3Y0 O1A PA DOUB N N 25 3Y0 O2A PA SING N N 26 3Y0 PN O3 SING N N 27 3Y0 PN O1N DOUB N N 28 3Y0 PN O2N SING N N 29 3Y0 O3 PA SING N N 30 3Y0 PA O5B SING N N 31 3Y0 O5B C5B SING N N 32 3Y0 C5B C4B SING N N 33 3Y0 C4B C3B SING N N 34 3Y0 C4B O4B SING N N 35 3Y0 C3B C2B SING N N 36 3Y0 C3B O3B SING N N 37 3Y0 O4B C1B SING N N 38 3Y0 C2B C1B SING N N 39 3Y0 C2B O2B SING N N 40 3Y0 C8A N7A DOUB Y N 41 3Y0 C8A N9A SING Y N 42 3Y0 C1B N9A SING N N 43 3Y0 N7A C5A SING Y N 44 3Y0 N9A C4A SING Y N 45 3Y0 C5A C4A DOUB Y N 46 3Y0 C5A C6A SING Y N 47 3Y0 C4A N3A SING Y N 48 3Y0 C6A N6A SING N N 49 3Y0 C6A N1A DOUB Y N 50 3Y0 N3A C2A DOUB Y N 51 3Y0 N1A C2A SING Y N 52 3Y0 O2N H1 SING N N 53 3Y0 C5B H2 SING N N 54 3Y0 C5B H3 SING N N 55 3Y0 C4B H4 SING N N 56 3Y0 C1B H5 SING N N 57 3Y0 C8A H6 SING N N 58 3Y0 N6A H7 SING N N 59 3Y0 N6A H8 SING N N 60 3Y0 C2A H9 SING N N 61 3Y0 C2B H10 SING N N 62 3Y0 O2B H11 SING N N 63 3Y0 C3B H12 SING N N 64 3Y0 O3B H13 SING N N 65 3Y0 O2A H14 SING N N 66 3Y0 C5D H15 SING N N 67 3Y0 C5D H16 SING N N 68 3Y0 C4D H17 SING N N 69 3Y0 C3D H18 SING N N 70 3Y0 O3D H19 SING N N 71 3Y0 C2D H20 SING N N 72 3Y0 C1D H21 SING N N 73 3Y0 S1 H22 SING N N 74 3Y0 C1 H23 SING N N 75 3Y0 C1 H24 SING N N 76 3Y0 C2 H25 SING N N 77 3Y0 C2 H26 SING N N 78 3Y0 C3 H27 SING N N 79 3Y0 C3 H28 SING N N 80 3Y0 C4 H29 SING N N 81 3Y0 C4 H30 SING N N 82 3Y0 C5 H31 SING N N 83 3Y0 C5 H32 SING N N 84 3Y0 C6 H33 SING N N 85 3Y0 C6 H34 SING N N 86 3Y0 C7 H35 SING N N 87 3Y0 C7 H36 SING N N 88 3Y0 C8 H37 SING N N 89 3Y0 C8 H38 SING N N 90 3Y0 C9 H39 SING N N 91 3Y0 C9 H40 SING N N 92 3Y0 C10 H41 SING N N 93 3Y0 C10 H42 SING N N 94 3Y0 C11 H43 SING N N 95 3Y0 C11 H44 SING N N 96 3Y0 C12 H45 SING N N 97 3Y0 C12 H46 SING N N 98 3Y0 C13 H47 SING N N 99 3Y0 C13 H48 SING N N 100 3Y0 C13 H49 SING N N 101 # loop_ _pdbx_chem_comp_descriptor.comp_id _pdbx_chem_comp_descriptor.type _pdbx_chem_comp_descriptor.program _pdbx_chem_comp_descriptor.program_version _pdbx_chem_comp_descriptor.descriptor 3Y0 SMILES ACDLabs 12.01 "O=P(OCC3OC(n1c2ncnc(N)c2nc1)C(O)C3O)(O)OP(=O)(O)OCC4OC(S)C(OCCCCCCCCCCCCC)C4O" 3Y0 InChI InChI 1.03 ;InChI=1S/C28H49N5O13P2S/c1-2-3-4-5-6-7-8-9-10-11-12-13-41-24-22(35)19(45-28(24)49)15-43-48(39,40)46-47(37,38)42-14-18-21(34)23(36)27(44-18)33-17-32-20-25(29)30-16-31-26(20)33/h16-19,21-24,27-28,34-36,49H,2-15H2,1H3,(H,37,38)(H,39,40)(H2,29,30,31)/t18-,19-,21-,22-,23-,24-,27-,28-/m1/s1 ; 3Y0 InChIKey InChI 1.03 VSVPTUFDWKYDGH-VBLNILRESA-N 3Y0 SMILES_CANONICAL CACTVS 3.385 "CCCCCCCCCCCCCO[C@H]1[C@@H](S)O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4c(N)ncnc34)[C@H]1O" 3Y0 SMILES CACTVS 3.385 "CCCCCCCCCCCCCO[CH]1[CH](S)O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)n3cnc4c(N)ncnc34)[CH]1O" 3Y0 SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 "CCCCCCCCCCCCCO[C@@H]1[C@@H]([C@H](O[C@@H]1S)COP(=O)(O)OP(=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3ncnc4N)O)O)O" 3Y0 SMILES "OpenEye OEToolkits" 1.9.2 "CCCCCCCCCCCCCOC1C(C(OC1S)COP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)n3cnc4c3ncnc4N)O)O)O" # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier 3Y0 "SYSTEMATIC NAME" ACDLabs 12.01 "[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3R,4R,5R)-3-hydroxy-5-sulfanyl-4-(tridecyloxy)tetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)" 3Y0 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 "[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3R,4R,5R)-3-oxidanyl-5-sulfanyl-4-tridecoxy-oxolan-2-yl]methyl hydrogen phosphate" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 3Y0 "Create component" 2014-12-09 PDBJ 3Y0 "Initial release" 2016-01-13 RCSB #